Meh, Bogota should be a later down the list Spanish city, as should Panama, etc. Same goes for Rio and Bahia with Portugal. As for the Mayan cities, their dis-inclusion almost guarantees they'll be DLC at some point.
Tlaxcala - Should be Military. Allied with the Spanish to defeat the Aztecs. Were never conquered by the Aztecs themselves, but were "farmed" for sacrificial victims.
Teotihuacan - THE Ur-Central Mexican Valley state
Monte Alban - this feature was made for them
Cohokia - dito
Moche and Tiwanaku - pre-Inca, and important ceremonial Andean centers
Benin - c'mon - show some love! - I've always wanted them in some form in a Civ game ever since I saw a traveling exhibition of their art as a child.
Oyo and Ife - the two most important Yoruba city states: former Militaristic, later cultural.
Kongo would be a great central African fit.
Great Zimbabwe - the major historical Southern African center - give Capetown to the Dutch!
Kilwa was the major Swahili coastal city.
Zanzibar - no brainer. Where are they?
Napata or Meroë - although I hope the Nubians get added later as a civ finally.
Axum - If they're gonna be dicks and not add the Ethiopians within a year, or at all!!!
Kano - was the most important Hausa city state, and the Songhai even conquered and held it for a brief period.
Byblos - Why only Sidon and Tyre?
Palmyra - even temporarily held a quarter of the Roman empire.
Angkor - with Siam in, I doubt that the Khmer will be added as a whole civ.
Pagan - early Burmese city-synonymous kingdom
Malacca - Seriously were are these guys? They should be the Malayan one, not Kuala Lumpur!
Majapahit - if they're not gonna be a civ - need something Javanese (Bantam and yes, Jakarta, would work as well)
Ghent, Antwerp, Zurich, Danzig, etc. - to replace the modern Euro-Nation capitals.
Krakow - Instead of Warsaw. It was actualy a city-state in the 19th cent. for a while.
Kiev - after the collapse of Kievan Rus, functioned as a semi-city state paying tribute to various groups.
